Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis
Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain re...
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| Published in | Molecular systems biology Vol. 18; no. 9; pp. e11080 - n/a |
|---|---|
| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
01.09.2022
EMBO Press John Wiley and Sons Inc Springer Nature |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1744-4292 1744-4292 |
| DOI | 10.15252/msb.202211080 |
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| Abstract | Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease.
In silico
spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high‐resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology‐specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain.
Synopsis
Vesalius is a computational tool for recovering tissue territories from spatial transcriptomics data using image processing technology. Vesalius illustrates how uniform tissue territories can help understanding tissue heterogeneity.
Vesalius leverages image analysis to investigate spatial transcriptomics data by embedding the transcriptome into RGB image arrays.
Vesalius provides uniform tissue territories from high resolution spatial transcriptomics data.
Downstream analysis of isolated tissue territories reveals the finer details of spatial patterning as well as tissue specific gene expression within cell types.
Graphical Abstract
Vesalius is a computational tool for recovering tissue territories from spatial transcriptomics data using image processing technology. Vesalius illustrates how uniform tissue territories can help understanding tissue heterogeneity. |
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| AbstractList | Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high‐resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology‐specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain. Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high‐resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology‐specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain. Vesalius is a computational tool for recovering tissue territories from spatial transcriptomics data using image processing technology. Vesalius illustrates how uniform tissue territories can help understanding tissue heterogeneity. Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high-resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology-specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain.Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high-resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology-specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain. Abstract Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high‐resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology‐specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain. Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high‐resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology‐specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain. Synopsis Vesalius is a computational tool for recovering tissue territories from spatial transcriptomics data using image processing technology. Vesalius illustrates how uniform tissue territories can help understanding tissue heterogeneity. Vesalius leverages image analysis to investigate spatial transcriptomics data by embedding the transcriptome into RGB image arrays. Vesalius provides uniform tissue territories from high resolution spatial transcriptomics data. Downstream analysis of isolated tissue territories reveals the finer details of spatial patterning as well as tissue specific gene expression within cell types. Graphical Abstract Vesalius is a computational tool for recovering tissue territories from spatial transcriptomics data using image processing technology. Vesalius illustrates how uniform tissue territories can help understanding tissue heterogeneity. Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high‐resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology‐specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain. Synopsis Vesalius is a computational tool for recovering tissue territories from spatial transcriptomics data using image processing technology. Vesalius illustrates how uniform tissue territories can help understanding tissue heterogeneity. Vesalius leverages image analysis to investigate spatial transcriptomics data by embedding the transcriptome into RGB image arrays. Vesalius provides uniform tissue territories from high resolution spatial transcriptomics data. Downstream analysis of isolated tissue territories reveals the finer details of spatial patterning as well as tissue specific gene expression within cell types. Vesalius is a computational tool for recovering tissue territories from spatial transcriptomics data using image processing technology. Vesalius illustrates how uniform tissue territories can help understanding tissue heterogeneity. |
| Author | Martin, Patrick C N Lövkvist, Cecilia Won, Kyoung Jae Kim, Hyobin Hong, Byung‐Woo |
| AuthorAffiliation | 2 Biotech Research and Innovation Centre (BRIC) University of Copenhagen Copenhagen Denmark 3 Computer Science Department Chung‐Ang University Seoul Korea 1 Department of Computational Biomedicine Cedars‐Sinai Medical Center Hollywood CA USA |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/36065846$$D View this record in MEDLINE/PubMed |
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| CitedBy_id | crossref_primary_10_1016_j_drudis_2024_103889 crossref_primary_10_1016_j_crmeth_2024_100838 crossref_primary_10_1038_s41467_023_40068_5 crossref_primary_10_1007_s11427_023_2561_0 crossref_primary_10_1093_bib_bbad197 crossref_primary_10_1093_bib_bbae052 |
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| Keywords | tissue heterogeneity spatial domains tissue architecture anatomical territories spatial transcriptomics |
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| Snippet | Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease.
In silico
spatial domain retrieval... Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval... Abstract Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain... |
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| StartPage | e11080 |
| SubjectTerms | anatomical territories Animals Astrocytes Bar codes Brain Cell interactions Colon Datasets Domains EMBO10 EMBO22 Gene expression Image analysis Image processing Medical imaging Method Methods Mice Morphology Oligodendrocytes Retrieval Spatial data spatial domains spatial transcriptomics tissue architecture tissue heterogeneity Tissues Transcriptome - genetics Transcriptomics |
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| Title | Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis |
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